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Access to vocabulary mapping file


I’m hoping someone can point me in the right direction. I’m working on a project where we want to map a subset of the ICD10CM and ICD10PCS to SNOMED. We’ve pulled the mappings available in the UMLS, but, there is a large number of codes in our subset that have no mappings there.
We have subsets of ICD9 and MedDRA to map as well.

Is there a way that we can download or programmatically access the mappings that I can see via ATHENA?

Thanks in advance for your help!

(Anna Karenina) #2

Hello @lms,

You can download OMOP Vocabularies from Athena in CSV files:

  1. You’ll need to create an Athena account first.
  2. After logging in, go to Downloads page (link in header), select the vocabs that you need and click “Download vocabularies”.
  3. Athena will prepare your vocabulary bundle and then you can download it. Link is also sent to e-mail.

DDL for vocabulary tables can be found in CDM repo:


We will try it; thank you!


If we want the ICD9 to SNOMED and ICD10CM to SNOMED mappings, then do we need to download all 3 vocabularies (ICD9, ICD10CM, and SNOMED)?

(Dmytry Dymshyts) #5